<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<html>
<head>
  <link rel="stylesheet" type="text/css" href="RD.css">
  <meta content="text/html; charset=ISO-8859-1"
 http-equiv="content-type">
   <title>Generating Structures</title>
</head>
<body>

<h2>
<!--
<Object type="application/x-oleobject" classid="clsid:1e2a7bd0-dab9-11d0-b93a-00c04fc99f9e">
	<param name="Keyword" value="alignment">
	<param name="Keyword" value="cleaning structures">
	<param name="Keyword" value="bounds matrix, embedding">
	<param name="Keyword" value="generating structures">
</OBJECT> -->
<a name="Generating_Structures"></a>Generating Structures</h2>
Three-dimensional structures are generated for a mapping by:<br>
<ol>
  <li>Creating an initial set of coordinates by embedding the updated
bounds matrix for each mapping [<a href="References.htm#Crippen1981">Crippen1981</a>]</li>
  <li>Cleaning up the embedded structures using the Universal Force
Field (UFF).[<a href="References.htm#Rappe1992">Rappe1992</a>, <a
 href="References.htm#Casewit1992">Casewit1992</a>] The
optimization is done with constraints to ensure that the final
structure still satisfies the pharmacophore.</li>
  <li>Aligning the cleaned conformation to the reference pharmacophore.[<a
 href="References.htm#Heisterberg1990">Heisterberg1990</a>]</li>
</ol>
Whenever possible, multiple aligned conformations are generated for
each mapping. This provides the user with an overview of the ways in
which the probe molecule can satisfy the pharmacophore.&lt;&gt;<br>

</body>
</html>